+

US7256179B2 - Nucleic acid-based compounds and methods of use thereof - Google Patents

Nucleic acid-based compounds and methods of use thereof Download PDF

Info

Publication number
US7256179B2
US7256179B2 US11/057,779 US5777905A US7256179B2 US 7256179 B2 US7256179 B2 US 7256179B2 US 5777905 A US5777905 A US 5777905A US 7256179 B2 US7256179 B2 US 7256179B2
Authority
US
United States
Prior art keywords
pharmaceutical composition
compounds
compound
pharmaceutically acceptable
group
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Expired - Lifetime
Application number
US11/057,779
Other versions
US20050143337A1 (en
Inventor
Radhakrishnan P. Iyer
Yi Jin
Arlene Roland
Wenqiang Zhou
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Biowest Therapeutics Inc
Original Assignee
Migenix Inc
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Migenix Inc filed Critical Migenix Inc
Priority to US11/057,779 priority Critical patent/US7256179B2/en
Publication of US20050143337A1 publication Critical patent/US20050143337A1/en
Priority to US11/775,591 priority patent/US7709449B2/en
Application granted granted Critical
Publication of US7256179B2 publication Critical patent/US7256179B2/en
Anticipated expiration legal-status Critical
Expired - Lifetime legal-status Critical Current

Links

Classifications

    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
    • C07H21/00—Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
    • C07H21/04—Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids with deoxyribosyl as saccharide radical
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/70—Carbohydrates; Sugars; Derivatives thereof
    • A61K31/7088—Compounds having three or more nucleosides or nucleotides
    • A61K31/713—Double-stranded nucleic acids or oligonucleotides
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P1/00—Drugs for disorders of the alimentary tract or the digestive system
    • A61P1/16—Drugs for disorders of the alimentary tract or the digestive system for liver or gallbladder disorders, e.g. hepatoprotective agents, cholagogues, litholytics
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
    • A61P31/12—Antivirals
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
    • A61P31/12—Antivirals
    • A61P31/20—Antivirals for DNA viruses
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
    • C07H19/00—Compounds containing a hetero ring sharing one ring hetero atom with a saccharide radical; Nucleosides; Mononucleotides; Anhydro-derivatives thereof
    • C07H19/02—Compounds containing a hetero ring sharing one ring hetero atom with a saccharide radical; Nucleosides; Mononucleotides; Anhydro-derivatives thereof sharing nitrogen
    • C07H19/04—Heterocyclic radicals containing only nitrogen atoms as ring hetero atom
    • C07H19/06—Pyrimidine radicals
    • C07H19/10—Pyrimidine radicals with the saccharide radical esterified by phosphoric or polyphosphoric acids
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
    • C07H19/00—Compounds containing a hetero ring sharing one ring hetero atom with a saccharide radical; Nucleosides; Mononucleotides; Anhydro-derivatives thereof
    • C07H19/02—Compounds containing a hetero ring sharing one ring hetero atom with a saccharide radical; Nucleosides; Mononucleotides; Anhydro-derivatives thereof sharing nitrogen
    • C07H19/04—Heterocyclic radicals containing only nitrogen atoms as ring hetero atom
    • C07H19/16—Purine radicals
    • C07H19/20—Purine radicals with the saccharide radical esterified by phosphoric or polyphosphoric acids
    • C07H19/207—Purine radicals with the saccharide radical esterified by phosphoric or polyphosphoric acids the phosphoric or polyphosphoric acids being esterified by a further hydroxylic compound, e.g. flavine adenine dinucleotide or nicotinamide-adenine dinucleotide
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
    • C07H21/00—Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids

Definitions

  • the present invention relates to nucleic-acid based compounds.
  • Compounds of the invention are useful for a variety of therapeutic applications, including treatment against hepatitis B virus.
  • Hepatitis B virus is a compact, enveloped DNA virus belonging to the Hepadnavirus family. The virus is a major cause of chronic liver disease and hepatocellular carcinoma worldwide (Hoofnagle (1990) N. Eng. J. Med ., 323:337-339). HBV is associated with acute and chronic hepatitis and hepatocellular carcinoma and may be a cofactor in the development of acquired immune deficiency syndrome (Dinestag et al. in Harrison's Principles of Internal Medicine, 13 th Ed. (Isselbacher et al. eds.) McGrw-Hill, NY, N.Y. (1993) pp. 1458-1483). At least 400 million people are currently infected with HBV.
  • Compounds of the invention are nucleic-based small molecules that contain at least two nucleoside units, and typically contain no more than about 2, 3, 4, 5 or 6 nucleotide units, preferably no more than about 2, 3, or 4 nucleotide units, still more preferably a total of 2 or 3 nucleoside units.
  • Compounds of the invention comprise at least one nucleotide unit that contains one or more modifications from “natural” nucleic acids.
  • Preferred compounds of the invention include those that have phosphorothioate and/or phophoramidate internucleotide linkages.
  • Especially preferred compounds of the invention include the following compounds 1, 2 and 3, and pharmaceutically acceptable salts of such compounds:
  • the invention also includes therapeutic methods comprising use of one or more compounds of the invention.
  • Methods of the invention include treatment of HBV infections, including treatment and prevention (prophylactic therapy) of HBV-associated disorders or diseases.
  • Preferred methods of the invention include administering a therapeutic effective amount of a compound of the invention to a viral infected cell, particularly a human cell, especially a cell that is infected with HBV.
  • Methods of the invention also comprise administering to a mammal, particularly a primate such as a human, an effective amount of one or more compounds of the invention.
  • the invention further provides pharmaceutical compositions that comprise one or more compound of the invention and a pharmaceutically acceptable carrier.
  • Compounds of the invention comprise one or more modifications from “natural” nucleic acids, i.e. natural internucleoside linkages, bases of G, C, T and U, etc. Modifications include, for example, modifications of the internucleotide linkage, the base or the sugar moiety, etc.
  • Compounds of the invention suitably contain two or more deoxyribonucleotide and/or ribonucleotide monomers connected by internucleotide linkages.
  • Compounds of the invention may be constructed entirely of deoxyribonucleotides, entirely of ribonucleotides or of a combination of deoxyribonucleotides and ribonucleotides, including hybrid and inverted hybrid compounds.
  • Hybrid compounds contain a core region (e.g. 1, 2 or 3 units) of deoxyribonucleotides interposed between flanking regions of ribonucleotides (e.g. 1, 2 or 3 units).
  • Inverted hybrids contain a core region of ribonucleotides (e.g. 1, 2, or 3 units) interposed between flanking regions of deoxyribonucleotides (e.g. 1, 2 or 3 units).
  • Nucleotide units of compounds of the invention may be connected by standard phosphodiester internucleotide linkages between the 5′ group of one mononucleotide pentose ring and the 3′ group of an adjacent mononucleotide. Such linkages could also be established using different sites of connection, including 5′ to 5′, 3′ to 3′, 2′ to 5′ and 2′ to 2′, or any combination thereof.
  • the mononucleotides may also be connected by alkylphosphonate, phosphorothioate, phosphorodithioate, alkylphosphonothioate, phosphoramidate, carbamate, carbonate, phosphate triester, acetamidate, or carboxymethyl ester linkages, or any combination thereof.
  • preferred compounds of the invention include at least one phosphorothioate and/or phosphoramidate linkage.
  • Compounds of the invention may be constructed such that all mononucleotides units (e.g. 2, 3, 4, 5 or 6 total units) are connected by the same type of internucleotide linkages or by combinations of different internucleotide linkages, including chimeric or inverted chimeric oligonucleotides.
  • Chimeric compounds of the invention have a phosphorothioate core region interposed between methylphosphonate or phosphoramidate flanking regions.
  • Inverted chimeric compounds of the invention have a nonionic core region (e.g. alkylphosphonate and/or phosphoramidate and/or phosphotriester internucleoside linkage) interposed between phosphorothioate flanking regions.
  • Compounds of the invention also may be constructed of adenine, cytosine, guanine, inosine, thymidine or uracil mononucleotides.
  • Preferred compounds of the invention may be constructed from mononucleotide units which contain modifications to the base and/or sugar moiety of the mononucleotide. Modifications to the base or sugar include covalently attached substituents of alkyl, carbocyclic aryl, heteroaromatic or heteroalicyclic groups having from 1 to 3 separate or fused rings and 1 to 3 N, O or S atoms, or a heterocyclic structure.
  • Alkyl groups preferably contain from 1 to about 18 carbon atoms, more preferably from 1 to about 12 carbon atoms and most preferably from 1 to about 6 carbon atoms.
  • Specific examples of alkyl groups include, for example, methyl, ethyl, n-propyl, isopropyl, n-butyl, t-butyl, isobutyl, pentyl, hexyl, heptyl, octyl, nonyl, decyl etc.
  • Aralkyl groups include the above-listed alkyl groups substituted by a carbocyclic aryl group having 6 or more carbons, for example, phenyl, naphthyl, phenanthryl, anthracyl, etc.
  • Cycloalkyl groups preferably have from 3 to about 8 ring carbon atoms, e.g. cyclopropyl, cyclopentyl, cyclohexyl, cycloheptyl, 1,4-methylenecyclohexane, adamantyl, cyclopentylmethyl, cyclohexylmethyl, 1- or 2-cyclohexylethyl and 1-, 2- or 3-cyclohexylpropyl, etc.
  • ring carbon atoms e.g. cyclopropyl, cyclopentyl, cyclohexyl, cycloheptyl, 1,4-methylenecyclohexane, adamantyl, cyclopentylmethyl, cyclohexylmethyl, 1- or 2-cyclohexylethyl and 1-, 2- or 3-cyclohexylpropyl, etc.
  • heteroaromatic and heteroalicyclic group include pyridyl, pyrazinyl, pyrimidyl, furyl, pyrrolyl, thienyl, thiazolyl, oxazolyl, imidazolyl, indolyl, benzothiazolyl, tetrahydrofuranyl, tetrahydropyranyl, piperidinyl, morpholino and pyrrolidinyl.
  • Preferred modifications to the sugar group include modifications to the 2′ position of the ribose moiety which include but are not limited to 2′—O-substituted with an —O-lower alkyl group containing 1-6 saturated or unsaturated carbon atoms, or with an —O-aryl, or allyl group having 2-6 carbon atoms wherein such —O-alkyl, aryl or allyl group may be unsubstituted or may be substituted (e.g., with halogen, hydroxy, trifluoromethyl, cyano, nitro, acyl, acyloxy, alkoxy, carboxy, carbalkoxyl, or amino groups), or wherein the 2′—O-group is substituted by an amino, or halogen group. None of these substitutions are intended to exclude the native 2′-hydroxyl group in case of ribose or 2′—H— in the case of deoxyribose.
  • Preferred compounds of the invention having modified nucleotide units include 2′—O-methyl ribonucleotides (2′—OMe) and 5-methylated deoxycytosine (5-Me-dC).
  • Particularly preferred compounds of the invention comprises at least one, preferably one to five 2′—O-methyl ribonucleotides at the 3′ end of the oligonucleotide.
  • a compound of the invention may further comprise at least one, preferably one to five 2′—O-methyl ribonucleotides at the 5′-end.
  • Sugar groups of mononucleotide units of compounds of the invention may be natural or modified (e.g. synthetic) and in an open chain or ring form.
  • Sugar groups may be comprised of mono-, di-, oligo- or poly-saccharides wherein each monosaccharide unit comprises from 3 to about 8 carbons, preferably from 3 to about 6 carbons, containing polyhydroxy groups or polyhydroxy and amino groups.
  • Non-limiting examples include glycerol, ribose, fructose, glucose, glucosamine, mannose, galactose, maltose, cellobiose, sucrose, starch, amylose, amylopectin, glycogen and cellulose.
  • hydroxyl and amino groups are present as free or protected groups containing e.g. hydrogens and/or halogens.
  • Preferred protecting groups include acetonide, t-butoxy carbonyl groups, etc.
  • Monosaccharide sugar groups may be of the L or D configuration and a cyclic monosaccharide unit may contain a 5 or 6 membered ring of the ⁇ or ⁇ conformation.
  • Disaccharides may be comprised of two identical or two dissimilar monosaccharide units. Oligosaccharides may be comprised of from 2 to 10 monosaccharides and may be homopolymers, heteropolymers or cyclic polysugars. Polysaccharides may be homoglycans or heteroglycans and may be branched or unbranched polymeric chains.
  • the di-, oligo- and poly-saccharides may be comprised of 1 4, 1 6 or a mixture of 1 4 and 1 6 linkages.
  • the sugar moiety may be attached to the link group through any of the hydroxyl or amino groups of the carbohydrate.
  • modifications include those which are internal or are at the end(s) of a compound of the invention and include additions to the molecule at the internucleoside phosphate linkages, such as cholesterol, cholesterol or diamine compounds with varying numbers of carbon residues between the two amino groups, and terminal ribose, deoxyribose and phosphate modifications which cleave, or crosslink to the opposite chains or to associated enzymes or other proteins which bind to the viral genome.
  • Additional linkers including non-nucleoside linkers include, but are not limited to, polyethylene glycol of varying lengths, e.g., triethylene glycol, monoethylene glycol, hexaethylene glycol, (Ma et al. (1993) Nucleic Acids Res .
  • Amination may include but is not limited to the following moieties, spermine, spermidine, Tris(2-aminoethyl) amine (TAEA), DOPE, long chain alkyl amines, crownethers, coenzyme A, NAD, sugars, peptides, dendrimers.
  • Compounds of the invention also may be capped with a bulky substituent at their 3′ and/or 5′ end(s), or have a substitution in one or both nonbridging oxygens per nucleotide.
  • Such modifications can be at some or all of the internucleoside linkages, as well as at either or both ends of the oligonucleotide and/or in the interior of the molecule (reviewed in Agrawal et al. (1992) Trends Biotechnol . 10: 152-158).
  • Some non-limited examples of capped species include 3′—O-methyl, 5′—O-methyl, 2′—O-methyl, and any combination thereof.
  • Specifically preferred compounds of the invention include the following compounds 1 through 62:
  • nucleotide units can be covalently linked using art-recognized techniques such as phosphoramidite, H-phosphonate chemistry, or methylphosphoramidite chemistry (see, e.g., Goodchild (1990) Bioconjugate Chem . 2: 165-187; Uhlmann et al. (1990) Chem. Rev . 90: 543-584; Caruthers et al. (1987) Meth. Enzymol . 154: 287-313; U.S. Pat. No. 5,149,798) which can be carried out manually or by an automated synthesizer and then processed (reviewed in Agrawal et al.
  • art-recognized techniques such as phosphoramidite, H-phosphonate chemistry, or methylphosphoramidite chemistry
  • Oligonucleotides with other types of modified internucleotide linkages can be prepared according to known methods (see, e.g., Goodchild (1990) Bioconjugate Chem . 2: 165-187; Agrawal et al. (1988) Proc. Natl. Acad. Sci . (USA) 85: 7079-7083; Uhlmann et al. (1990) Chem. Rev . 90: 534-583; and Agrawal et al. (1992) Trends Biotechnol . 10: 152-158).
  • the invention provides a pharmaceutical composition which comprises at least one compound of the invention, preferably together with a pharmaceutically acceptable carrier.
  • a pharmaceutically acceptable carrier include a therapeutic amount of a lipid carrier.
  • compounds of the invention are suitable for use in a variety of therapeutic application, particularly to treat against a viral infection in mammalian cells, particularly human cells.
  • Compounds of the invention are especially for use in the control or prevention of hepatisis viruses, particularly control or prevention of hepatitis B viral infections in human cells.
  • Compounds of the invention also are useful to treat against drug-resistant viral strains, including strains of hepatitis B virus that are resistant to current therapies.
  • Preferred therapeutic methods of the invention include administering a therapeutic amount of a pharmaceutical composition containing one or more compounds of the invention to a cell to thereby inhibit or otherwise treat against a hepatitis B viral infection.
  • compounds of the invention can be used for treating hepatitis B viral infections comprising the step of administering to an infected cell or animal, particularly a primate such as a human, a therapeutic amount of a pharmaceutical composition containing at least one compounds of the invention.
  • Compounds of the invention may be used in therapy in conjunction with other medicaments such as reverse transcriptase inhibitors such as a dideoxynucleoside e.g. 3TC.
  • reverse transcriptase inhibitors such as a dideoxynucleoside e.g. 3TC.
  • administration of multiple, distinct compounds of the invention to a subject as part of a coordinated therapeutic regime is particularly preferred. Particularly preferred is where at least two or more preferably all three of compounds 1, 2 and 3 are administered to a patient as part of a coordinated administration regime.
  • Such combination therapy i.e. of a compound of the invention either with a distinct agent such as 3Tc, or with an additional compound of the invention may be accomplished by administration of the same or different pharmaceutical formulations, or sequential administration of the distinct agents.
  • a distinct agent such as 3Tc
  • sequential administration of the distinct agents Generally preferred however is the substantially simultaneous of multiple distinct agents to a patient, e.g. in a unitary pharmaceutical composition containing the compounds.
  • Administration of compounds of the invention may be made by a variety of suitable routes including oral, topical (including transdermal, buccal or sublingal), nasal and parenteral (including intraperitoneal, subcutaneous, intravenous, intradermal or intramuscular injection) with oral or parenteral being generally preferred. It also will be appreciated that the preferred method of administration and dosage amount may vary with, for example, the condition and age of the recipient.
  • Compounds of the invention may be used in therapy in conjunction with other pharmaceutically active medicaments, such as another anti-viral agent, or an anti-cancer agent. Additionally, while one or more compounds of the invention may be administered alone, they also may be present as part of a pharmaceutical composition in mixture with conventional excipient, i.e., pharmaceutically acceptable organic or inorganic carrier substances suitable for parenteral, oral or other desired administration and which do not deleteriously react with the active compounds and are not deleterious to the recipient thereof.
  • conventional excipient i.e., pharmaceutically acceptable organic or inorganic carrier substances suitable for parenteral, oral or other desired administration and which do not deleteriously react with the active compounds and are not deleterious to the recipient thereof.
  • Suitable pharmaceutically acceptable carriers include but are not limited to water, salt solutions, alcohol, vegetable oils, polyethylene glycols, gelatin, lactose, amylose, magnesium stearate, talc, silicic acid, viscous paraffin, perfume oil, fatty acid monoglycerides and diglycerides, petroethral fatty acid esters, hydroxymethyl-cellulose, polyvinylpyrrolidone, etc.
  • the pharmaceutical preparations can be sterilized and if desired mixed with auxiliary agents, e.g., lubricants, preservatives, stabilizers, wetting agents, emulsifiers, salts for influencing osmotic pressure, buffers, colorings, flavorings and/or aromatic substances and the like which do not deleteriously react with the active compounds.
  • auxiliary agents e.g., lubricants, preservatives, stabilizers, wetting agents, emulsifiers, salts for influencing osmotic pressure, buffers, colorings, flavorings and/or aromatic substances and the like which do not deleteriously react with the active compounds.
  • solutions preferably oily or aqueous solutions as well as suspensions, emulsions, or implants, including suppositories.
  • Ampules are convenient unit dosages.
  • tablets, dragees or capsules having talc and/or carbohydrate carrier binder or the like are particularly suitable, the carrier preferably being lactose and/or corn starch and/or potato starch.
  • a syrup, elixir or the like can be used wherein a sweetened vehicle is employed.
  • Sustained release compositions can be formulated including those wherein the active component is protected with differentially degradable coatings, e.g., by microencapsulation, multiple coatings, etc.
  • Therapeutic compounds of the invention also may be incorporated into liposomes.
  • the incorporation can be carried out according to known liposome preparation procedures, e.g. sonication and extrusion. Suitable conventional methods of liposome preparation are also disclosed in e.g. A. D. Bangham et al., J. Mol. Biol ., 23: 238-252 (1965); F. Olson et al., Biochim. Biophys. Acta , 557: 9-23 (1979); F. Szoka et al., Proc. Nat. Acad. Sci ., 75:4194-4198 (1978); S. Kim et al., Biochim. Biophys. Acta , 728: 339-348 (1983); and Mayer et al., Biochim. Biophys. Acta , 858: 161-168 (1986).
  • HBV-infected human cells 2.2.15 cells infected were treated (in vitro) with compounds of the invention.
  • Significant depressions greater than 2-fold relative to the control
  • extracellular (virion) HBV DNA levels produced by the cells were observed for the above compounds, including compounds 1, 2 and 3.

Landscapes

  • Health & Medical Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Organic Chemistry (AREA)
  • Molecular Biology (AREA)
  • General Health & Medical Sciences (AREA)
  • Biochemistry (AREA)
  • Engineering & Computer Science (AREA)
  • Biotechnology (AREA)
  • Veterinary Medicine (AREA)
  • Public Health (AREA)
  • Medicinal Chemistry (AREA)
  • Animal Behavior & Ethology (AREA)
  • Pharmacology & Pharmacy (AREA)
  • Genetics & Genomics (AREA)
  • Virology (AREA)
  • Nuclear Medicine, Radiotherapy & Molecular Imaging (AREA)
  • General Chemical & Material Sciences (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Epidemiology (AREA)
  • Oncology (AREA)
  • Communicable Diseases (AREA)
  • Gastroenterology & Hepatology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Pharmaceuticals Containing Other Organic And Inorganic Compounds (AREA)
  • Saccharide Compounds (AREA)
  • Medicines That Contain Protein Lipid Enzymes And Other Medicines (AREA)
  • Micro-Organisms Or Cultivation Processes Thereof (AREA)

Abstract

The invention provides compounds capable of treating against hepatitis infections, particularly hepatitis B viral infections. Compounds of the invention are nucleic acid-based and preferably comprise 2, 3, 4, 5 or 6 nucleoside units.

Description

RELATED APPLICATIONS
This application is a divisional of U.S. application Ser. No. 10/146,175, filed May 15, 2002 now U.S. Pat. No. 6,881,831, which claims the benefit of U.S. Provisional Application No. 60/291,471, filed on May 16, 2001. The entire teachings of the above applications are incorporated herein by reference.
FIELD OF THE INVENTION
The present invention relates to nucleic-acid based compounds. Compounds of the invention are useful for a variety of therapeutic applications, including treatment against hepatitis B virus.
BACKGROUND
Hepatitis B virus (HBV) is a compact, enveloped DNA virus belonging to the Hepadnavirus family. The virus is a major cause of chronic liver disease and hepatocellular carcinoma worldwide (Hoofnagle (1990) N. Eng. J. Med., 323:337-339). HBV is associated with acute and chronic hepatitis and hepatocellular carcinoma and may be a cofactor in the development of acquired immune deficiency syndrome (Dinestag et al. in Harrison's Principles of Internal Medicine, 13th Ed. (Isselbacher et al. eds.) McGrw-Hill, NY, N.Y. (1993) pp. 1458-1483). At least 400 million people are currently infected with HBV.
Current clinic agents, however, do not provide effective therapy or cure of HBV infections. Antiviral therapy with interferon has been used for chronic hepatitis, but has met with only partial success, and there complications from such therapy. Short term therapy with glucocorticoids may be beneficial in conjunction with interferon therapy, but long term treatment is limited by toxicological problems (Dinestag et al., supra).
It thus would be desirable to have new agents for treatment of viral infections. It would be particularly desirable to have new agents for treatment against hepatitis B viral infections.
SUMMARY OF THE INVENTION
We have now found compounds and compositions that are particularly useful for treatment of viral infections. Preferred compounds of the invention that can exhibit significant activity against hepatitis B virus.
Compounds of the invention are nucleic-based small molecules that contain at least two nucleoside units, and typically contain no more than about 2, 3, 4, 5 or 6 nucleotide units, preferably no more than about 2, 3, or 4 nucleotide units, still more preferably a total of 2 or 3 nucleoside units. Compounds of the invention comprise at least one nucleotide unit that contains one or more modifications from “natural” nucleic acids. Preferred compounds of the invention include those that have phosphorothioate and/or phophoramidate internucleotide linkages.
Especially preferred compounds of the invention include the following compounds 1, 2 and 3, and pharmaceutically acceptable salts of such compounds:
Figure US07256179-20070814-C00001
The invention also includes therapeutic methods comprising use of one or more compounds of the invention. Methods of the invention include treatment of HBV infections, including treatment and prevention (prophylactic therapy) of HBV-associated disorders or diseases.
Preferred methods of the invention include administering a therapeutic effective amount of a compound of the invention to a viral infected cell, particularly a human cell, especially a cell that is infected with HBV. Methods of the invention also comprise administering to a mammal, particularly a primate such as a human, an effective amount of one or more compounds of the invention.
The invention further provides pharmaceutical compositions that comprise one or more compound of the invention and a pharmaceutically acceptable carrier.
Other aspects of the invention are disclosed infra.
DETAILED DESCRIPTION OF THE INVENTION
As discussed above, we have discovered new synthetic oligonucleotides (at least two nucleotide units) that can exhibit significant anti-HBV activity.
Compounds of the invention comprise one or more modifications from “natural” nucleic acids, i.e. natural internucleoside linkages, bases of G, C, T and U, etc. Modifications include, for example, modifications of the internucleotide linkage, the base or the sugar moiety, etc.
Compounds of the invention suitably contain two or more deoxyribonucleotide and/or ribonucleotide monomers connected by internucleotide linkages. Compounds of the invention may be constructed entirely of deoxyribonucleotides, entirely of ribonucleotides or of a combination of deoxyribonucleotides and ribonucleotides, including hybrid and inverted hybrid compounds. Hybrid compounds contain a core region (e.g. 1, 2 or 3 units) of deoxyribonucleotides interposed between flanking regions of ribonucleotides (e.g. 1, 2 or 3 units). Inverted hybrids contain a core region of ribonucleotides (e.g. 1, 2, or 3 units) interposed between flanking regions of deoxyribonucleotides (e.g. 1, 2 or 3 units).
Nucleotide units of compounds of the invention may be connected by standard phosphodiester internucleotide linkages between the 5′ group of one mononucleotide pentose ring and the 3′ group of an adjacent mononucleotide. Such linkages could also be established using different sites of connection, including 5′ to 5′, 3′ to 3′, 2′ to 5′ and 2′ to 2′, or any combination thereof. In addition to phosphodiester linkages, the mononucleotides may also be connected by alkylphosphonate, phosphorothioate, phosphorodithioate, alkylphosphonothioate, phosphoramidate, carbamate, carbonate, phosphate triester, acetamidate, or carboxymethyl ester linkages, or any combination thereof. As discussed above, preferred compounds of the invention include at least one phosphorothioate and/or phosphoramidate linkage.
Compounds of the invention may be constructed such that all mononucleotides units (e.g. 2, 3, 4, 5 or 6 total units) are connected by the same type of internucleotide linkages or by combinations of different internucleotide linkages, including chimeric or inverted chimeric oligonucleotides. Chimeric compounds of the invention have a phosphorothioate core region interposed between methylphosphonate or phosphoramidate flanking regions. Inverted chimeric compounds of the invention have a nonionic core region (e.g. alkylphosphonate and/or phosphoramidate and/or phosphotriester internucleoside linkage) interposed between phosphorothioate flanking regions.
Compounds of the invention also may be constructed of adenine, cytosine, guanine, inosine, thymidine or uracil mononucleotides. Preferred compounds of the invention may be constructed from mononucleotide units which contain modifications to the base and/or sugar moiety of the mononucleotide. Modifications to the base or sugar include covalently attached substituents of alkyl, carbocyclic aryl, heteroaromatic or heteroalicyclic groups having from 1 to 3 separate or fused rings and 1 to 3 N, O or S atoms, or a heterocyclic structure.
Alkyl groups preferably contain from 1 to about 18 carbon atoms, more preferably from 1 to about 12 carbon atoms and most preferably from 1 to about 6 carbon atoms. Specific examples of alkyl groups include, for example, methyl, ethyl, n-propyl, isopropyl, n-butyl, t-butyl, isobutyl, pentyl, hexyl, heptyl, octyl, nonyl, decyl etc. Aralkyl groups include the above-listed alkyl groups substituted by a carbocyclic aryl group having 6 or more carbons, for example, phenyl, naphthyl, phenanthryl, anthracyl, etc.
Cycloalkyl groups preferably have from 3 to about 8 ring carbon atoms, e.g. cyclopropyl, cyclopentyl, cyclohexyl, cycloheptyl, 1,4-methylenecyclohexane, adamantyl, cyclopentylmethyl, cyclohexylmethyl, 1- or 2-cyclohexylethyl and 1-, 2- or 3-cyclohexylpropyl, etc.
Exemplary heteroaromatic and heteroalicyclic group include pyridyl, pyrazinyl, pyrimidyl, furyl, pyrrolyl, thienyl, thiazolyl, oxazolyl, imidazolyl, indolyl, benzothiazolyl, tetrahydrofuranyl, tetrahydropyranyl, piperidinyl, morpholino and pyrrolidinyl.
Preferred modifications to the sugar group include modifications to the 2′ position of the ribose moiety which include but are not limited to 2′—O-substituted with an —O-lower alkyl group containing 1-6 saturated or unsaturated carbon atoms, or with an —O-aryl, or allyl group having 2-6 carbon atoms wherein such —O-alkyl, aryl or allyl group may be unsubstituted or may be substituted (e.g., with halogen, hydroxy, trifluoromethyl, cyano, nitro, acyl, acyloxy, alkoxy, carboxy, carbalkoxyl, or amino groups), or wherein the 2′—O-group is substituted by an amino, or halogen group. None of these substitutions are intended to exclude the native 2′-hydroxyl group in case of ribose or 2′—H— in the case of deoxyribose.
Preferred compounds of the invention having modified nucleotide units include 2′—O-methyl ribonucleotides (2′—OMe) and 5-methylated deoxycytosine (5-Me-dC). Particularly preferred compounds of the invention comprises at least one, preferably one to five 2′—O-methyl ribonucleotides at the 3′ end of the oligonucleotide. Moreover, a compound of the invention may further comprise at least one, preferably one to five 2′—O-methyl ribonucleotides at the 5′-end.
Sugar groups of mononucleotide units of compounds of the invention may be natural or modified (e.g. synthetic) and in an open chain or ring form. Sugar groups may be comprised of mono-, di-, oligo- or poly-saccharides wherein each monosaccharide unit comprises from 3 to about 8 carbons, preferably from 3 to about 6 carbons, containing polyhydroxy groups or polyhydroxy and amino groups. Non-limiting examples include glycerol, ribose, fructose, glucose, glucosamine, mannose, galactose, maltose, cellobiose, sucrose, starch, amylose, amylopectin, glycogen and cellulose. The hydroxyl and amino groups are present as free or protected groups containing e.g. hydrogens and/or halogens. Preferred protecting groups include acetonide, t-butoxy carbonyl groups, etc. Monosaccharide sugar groups may be of the L or D configuration and a cyclic monosaccharide unit may contain a 5 or 6 membered ring of the α or β conformation. Disaccharides may be comprised of two identical or two dissimilar monosaccharide units. Oligosaccharides may be comprised of from 2 to 10 monosaccharides and may be homopolymers, heteropolymers or cyclic polysugars. Polysaccharides may be homoglycans or heteroglycans and may be branched or unbranched polymeric chains.
The di-, oligo- and poly-saccharides may be comprised of 1
Figure US07256179-20070814-P00001
4, 1
Figure US07256179-20070814-P00001
6 or a mixture of 1
Figure US07256179-20070814-P00001
4 and 1
Figure US07256179-20070814-P00001
6 linkages. The sugar moiety may be attached to the link group through any of the hydroxyl or amino groups of the carbohydrate.
Other modifications include those which are internal or are at the end(s) of a compound of the invention and include additions to the molecule at the internucleoside phosphate linkages, such as cholesterol, cholesterol or diamine compounds with varying numbers of carbon residues between the two amino groups, and terminal ribose, deoxyribose and phosphate modifications which cleave, or crosslink to the opposite chains or to associated enzymes or other proteins which bind to the viral genome. Additional linkers including non-nucleoside linkers include, but are not limited to, polyethylene glycol of varying lengths, e.g., triethylene glycol, monoethylene glycol, hexaethylene glycol, (Ma et al. (1993) Nucleic Acids Res. 21: 2585-2589; Benseler et al. (1993) J. Am. Chem. Soc. 115: 8483-8484), hexylamine, and stilbene (Letsinger et al, (1995) J. Am. Chem. Soc. 117: 7323-7328) or any other commercially available linker including abasic linkers or commercially available asymmetric and symmetric linkers (CloneTech, Palo Alto, Calif.) (e.g., Glen Research Product Catalog, Sterling, Va.).
Additionally compounds of the invention capped with ribose at the 3′ end of the oligonucleotide may be subjected to NaIO4 oxidation/reductive amination. Amination may include but is not limited to the following moieties, spermine, spermidine, Tris(2-aminoethyl) amine (TAEA), DOPE, long chain alkyl amines, crownethers, coenzyme A, NAD, sugars, peptides, dendrimers.
Compounds of the invention also may be capped with a bulky substituent at their 3′ and/or 5′ end(s), or have a substitution in one or both nonbridging oxygens per nucleotide. Such modifications can be at some or all of the internucleoside linkages, as well as at either or both ends of the oligonucleotide and/or in the interior of the molecule (reviewed in Agrawal et al. (1992) Trends Biotechnol. 10: 152-158). Some non-limited examples of capped species include 3′—O-methyl, 5′—O-methyl, 2′—O-methyl, and any combination thereof.
Specifically preferred compounds of the invention include the following compounds 1 through 62:
Figure US07256179-20070814-C00002
Figure US07256179-20070814-C00003
Figure US07256179-20070814-C00004
Figure US07256179-20070814-C00005
Figure US07256179-20070814-C00006
Figure US07256179-20070814-C00007
Figure US07256179-20070814-C00008
Figure US07256179-20070814-C00009
Figure US07256179-20070814-C00010
Figure US07256179-20070814-C00011
Figure US07256179-20070814-C00012
Figure US07256179-20070814-C00013
Figure US07256179-20070814-C00014
Figure US07256179-20070814-C00015
Figure US07256179-20070814-C00016
Figure US07256179-20070814-C00017
Figure US07256179-20070814-C00018
Figure US07256179-20070814-C00019
Compounds of the can be prepared by art recognized methods. For example, nucleotide units can be covalently linked using art-recognized techniques such as phosphoramidite, H-phosphonate chemistry, or methylphosphoramidite chemistry (see, e.g., Goodchild (1990) Bioconjugate Chem. 2: 165-187; Uhlmann et al. (1990) Chem. Rev. 90: 543-584; Caruthers et al. (1987) Meth. Enzymol. 154: 287-313; U.S. Pat. No. 5,149,798) which can be carried out manually or by an automated synthesizer and then processed (reviewed in Agrawal et al. (1992) Trends Biotechnol. 10: 152-158). Compounds of the invention with phosphorothioate linkages can be prepared using methods well known in the field such as phosphoramidite (see, e.g., Agrawal et al. (1988) Proc. Natl. Acad. Sci. (USA) 85: 7079-7083) or H-phosphonate (see, e.g., Froehler (1986) Tetrahedron Lett. 27: 5575-5578) chemistry. The synthetic methods described in Bergot et al. (J. Chromatog. (1992) 559: 35-42) can also be used. Oligonucleotides with other types of modified internucleotide linkages can be prepared according to known methods (see, e.g., Goodchild (1990) Bioconjugate Chem. 2: 165-187; Agrawal et al. (1988) Proc. Natl. Acad. Sci. (USA) 85: 7079-7083; Uhlmann et al. (1990) Chem. Rev. 90: 534-583; and Agrawal et al. (1992) Trends Biotechnol. 10: 152-158).
As discussed above, the invention provides a pharmaceutical composition which comprises at least one compound of the invention, preferably together with a pharmaceutically acceptable carrier. Specific embodiments include a therapeutic amount of a lipid carrier.
As discussed above, compounds of the invention are suitable for use in a variety of therapeutic application, particularly to treat against a viral infection in mammalian cells, particularly human cells. Compounds of the invention are especially for use in the control or prevention of hepatisis viruses, particularly control or prevention of hepatitis B viral infections in human cells.
Compounds of the invention also are useful to treat against drug-resistant viral strains, including strains of hepatitis B virus that are resistant to current therapies.
Preferred therapeutic methods of the invention include administering a therapeutic amount of a pharmaceutical composition containing one or more compounds of the invention to a cell to thereby inhibit or otherwise treat against a hepatitis B viral infection. In a similar aspect, compounds of the invention can be used for treating hepatitis B viral infections comprising the step of administering to an infected cell or animal, particularly a primate such as a human, a therapeutic amount of a pharmaceutical composition containing at least one compounds of the invention.
Compounds of the invention may be used in therapy in conjunction with other medicaments such as reverse transcriptase inhibitors such as a dideoxynucleoside e.g. 3TC.
Also preferred is administration of multiple, distinct compounds of the invention to a subject as part of a coordinated therapeutic regime. Particularly preferred is where at least two or more preferably all three of compounds 1, 2 and 3 are administered to a patient as part of a coordinated administration regime.
Such combination therapy, i.e. of a compound of the invention either with a distinct agent such as 3Tc, or with an additional compound of the invention may be accomplished by administration of the same or different pharmaceutical formulations, or sequential administration of the distinct agents. Generally preferred however is the substantially simultaneous of multiple distinct agents to a patient, e.g. in a unitary pharmaceutical composition containing the compounds.
Administration of compounds of the invention may be made by a variety of suitable routes including oral, topical (including transdermal, buccal or sublingal), nasal and parenteral (including intraperitoneal, subcutaneous, intravenous, intradermal or intramuscular injection) with oral or parenteral being generally preferred. It also will be appreciated that the preferred method of administration and dosage amount may vary with, for example, the condition and age of the recipient.
Compounds of the invention may be used in therapy in conjunction with other pharmaceutically active medicaments, such as another anti-viral agent, or an anti-cancer agent. Additionally, while one or more compounds of the invention may be administered alone, they also may be present as part of a pharmaceutical composition in mixture with conventional excipient, i.e., pharmaceutically acceptable organic or inorganic carrier substances suitable for parenteral, oral or other desired administration and which do not deleteriously react with the active compounds and are not deleterious to the recipient thereof. Suitable pharmaceutically acceptable carriers include but are not limited to water, salt solutions, alcohol, vegetable oils, polyethylene glycols, gelatin, lactose, amylose, magnesium stearate, talc, silicic acid, viscous paraffin, perfume oil, fatty acid monoglycerides and diglycerides, petroethral fatty acid esters, hydroxymethyl-cellulose, polyvinylpyrrolidone, etc. The pharmaceutical preparations can be sterilized and if desired mixed with auxiliary agents, e.g., lubricants, preservatives, stabilizers, wetting agents, emulsifiers, salts for influencing osmotic pressure, buffers, colorings, flavorings and/or aromatic substances and the like which do not deleteriously react with the active compounds.
For parenteral application, particularly suitable are solutions, preferably oily or aqueous solutions as well as suspensions, emulsions, or implants, including suppositories. Ampules are convenient unit dosages.
For enteral application, particularly suitable are tablets, dragees or capsules having talc and/or carbohydrate carrier binder or the like, the carrier preferably being lactose and/or corn starch and/or potato starch. A syrup, elixir or the like can be used wherein a sweetened vehicle is employed. Sustained release compositions can be formulated including those wherein the active component is protected with differentially degradable coatings, e.g., by microencapsulation, multiple coatings, etc.
Therapeutic compounds of the invention also may be incorporated into liposomes. The incorporation can be carried out according to known liposome preparation procedures, e.g. sonication and extrusion. Suitable conventional methods of liposome preparation are also disclosed in e.g. A. D. Bangham et al., J. Mol. Biol., 23: 238-252 (1965); F. Olson et al., Biochim. Biophys. Acta, 557: 9-23 (1979); F. Szoka et al., Proc. Nat. Acad. Sci., 75:4194-4198 (1978); S. Kim et al., Biochim. Biophys. Acta, 728: 339-348 (1983); and Mayer et al., Biochim. Biophys. Acta, 858: 161-168 (1986).
It will be appreciated that the actual preferred amounts of active compounds used in a given therapy will vary according to the specific compound being utilized, the particular compositions formulated, the mode of application, the particular site of administration, etc. Optimal administration rates for a given protocol of administration can be readily ascertained by those skilled in the art using conventional dosage determination tests.
All documents mentioned herein are incorporated herein by reference.
The present invention is further illustrated by the following examples. These examples are provided to aid in the understanding of the invention and are not to be construed as limitations thereof.
EXAMPLE 1 Synthesis of Compounds of the Invention
Compounds of the invention can be synthesized using standard phosphoramidite chemistry (Beaucage (1993) Meth. Mol. Biol. 20: 33-61) on either an ABI 394 DNA/RNA synthesizer (Perkin-Elmer, Foster City, Calif.), a Pharmacia Gene Assembler Plus (Pharmacia, Uppsala, Sweden) or a Gene Assembler Special (Pharmacia, Uppsala, Sweden) using the manufacturers' standard protocols and custom methods.
EXAMPLE 2 Biological Testing
HBV-infected human cells (2.2.15 cells) infected were treated (in vitro) with compounds of the invention. Significant depressions (greater than 2-fold relative to the control) in extracellular (virion) HBV DNA levels produced by the cells were observed for the above compounds, including compounds 1, 2 and 3.
The invention has been described in detail with reference to preferred embodiments thereof. However, it will be appreciated that those skilled in the art, upon consideration of this disclosure, may make modifications and improvements within the spirit and scope of the invention as set forth in the following claims.

Claims (24)

1. A compound having the structure of any one of compounds 1, 2, 4, 7-11, 13, 14 or 16-62, or a pharmaceutically acceptable salt thereof, wherein compounds 1, 2, 4, 7-11, 13, 14, and 16-62 have the following structures:
Figure US07256179-20070814-C00020
Figure US07256179-20070814-C00021
Figure US07256179-20070814-C00022
Figure US07256179-20070814-C00023
Figure US07256179-20070814-C00024
Figure US07256179-20070814-C00025
Figure US07256179-20070814-C00026
Figure US07256179-20070814-C00027
Figure US07256179-20070814-C00028
Figure US07256179-20070814-C00029
Figure US07256179-20070814-C00030
Figure US07256179-20070814-C00031
Figure US07256179-20070814-C00032
Figure US07256179-20070814-C00033
Figure US07256179-20070814-C00034
Figure US07256179-20070814-C00035
Figure US07256179-20070814-C00036
Figure US07256179-20070814-C00037
Figure US07256179-20070814-C00038
Figure US07256179-20070814-C00039
Figure US07256179-20070814-C00040
Figure US07256179-20070814-C00041
2. A pharmaceutical composition comprising the compound of claim 1 in combination with a pharmaceutically acceptable carrier.
3. The pharmaceutical composition of claim 2 wherein the pharmaceutically acceptable carrier comprises a lipid.
4. A pharmaceutical composition for treating a viral infection comprising a therapeutically effective amount of a compound of claim 1 in combination with a pharmaceutically acceptable carrier.
5. A pharmaceutical composition for treating an HBV infection comprising a therapeutically effective amount of a compound of claim 1 in combination with a pharmaceutically acceptable carrier.
6. A pharmaceutical composition for treating a viral infection comprising a therapeutically effective amount of a compound of claim 1 in combination with a therapeutically effective amount of a reverse transcriptase inhibitor and a pharmaceutically acceptable carrier.
7. A pharmaceutical composition of claim 6 wherein the reverse transcriptase inhibitor is 3TC.
8. A pharmaceutical composition of claim 5 wherein the HBV infection is a drug resistant HBV infection.
9. A compound selected from the group consisting of compounds 1-11, 13, 14, 16-18, 20-23, 25-28, 31-36, 38-42, 44, 46, 49-53, 56, 58, and 60-62, or a pharmaceutically acceptable salt thereof, wherein the compound is modified by the replacement of the internucleotide linkage with a different linkage selected from the group consisting of alkylphosphonate, phosphorothioate, phosphorodithioate, alkylphosphonothioate, phosphoroamidate, carbamate, carbonate, phosphate trimester, acetamidate, carboxymethyl ester linkages, and combinations thereof wherein the structures of compounds 3, 5, and 6 are as follows and wherein the structures of compounds 1, 2, 4, 7-11, 13, 14, 16-18, 20-23, 25-28, 31-36, 38-42, 44, 46, 49-53, 56, 58, and 60-62 are as set forth in claim 1:
Figure US07256179-20070814-C00042
10. A compound selected from the group consisting of compounds 1-11, 13, 14 and 16-62 as set forth in claim 1 or claim 9 or a pharmaceutically acceptable salt thereof, wherein the compound is modified by replacement of the moiety at the 2′ position of the sugar group with a different moiety selected from the group consisting of H, —OH, an amino group, a halogen group, a substituted or unsubstituted —O-lower alkyl group containing 1 to 6 saturated or unsaturated carbon atoms, a substituted or unsubstituted —O-aryl group having 2 to 6 carbons and a substituted or unsubstituted —O-allyl group having 2 to 6 carbon atoms.
11. A pharmaceutical composition comprising at least one compound selected from compounds 1, 2, and 4-11, 13, 14, 16-62 as set forth in claim 1 or claim 9 as specified above.
12. A pharmaceutical composition comprising a compound of claim 9 and a pharmaceutically acceptable carrier.
13. A pharmaceutical composition comprising a compound of claim 10 and a pharmaceutically acceptable carrier.
14. A method for treating a viral infection comprising administering to a patient an effective amount of a pharmaceutical composition of claim 11.
15. A method for treating an HBV infection comprising administering to a patient an effective amount of a pharmaceutical composition of claim 11.
16. A method for treating a viral infection comprising administering to a patient an effective amount of a pharmaceutical composition of claim 12.
17. A method for treating an HBV infection comprising administering to a patient an effective amount of a pharmaceutical composition of claim 12.
18. A method for treating a viral infection comprising administering to a patient an effective amount of a pharmaceutical composition of claim 13.
19. A method for treating an HBV infection comprising administering to a patient an effective amount of a pharmaceutical composition of claim 13.
20. A compound of claim 1 selected from compounds 18, 20, 31, 39, 50, 52, 60, or 61 having the structures as set forth in claim 1.
21. A pharmaceutical composition comprising at least one compound selected from compounds 19, 30, 45, 47, 54, or 57 having the structures as set forth in claim 1, or a pharmaceutically acceptable salt thereof, wherein the compound is modified by the replacement of the internucleotide linkage with a different linkage selected from the group consisting of alkylphosphonate, phosphorothioate, phosphorodithioate, alkylphosphonothioate, phosphoroamidate, carbamate, carbonate, phosphate trimester, acetamidate, carboxymethyl ester linkages, and combinations thereof.
22. A method for treating a viral infection comprising administering to a patient an effective amount of a pharmaceutical composition of claim 21.
23. A method for treating an HBV infection comprising administering to a patient an effective amount of a pharmaceutical composition of claim 21.
24. A compound selected from the group consisting of compounds 24, 29, 37, 43, 48, 55, and 59 having the structures as previously set forth in claim 1, or a pharmaceutically acceptable salt thereof, wherein the compound is modified by the replacement of the internucleotide linkage with a different linkage selected from the group consisting of alkylphosphonate, phosphorodithioate, alkylphosphonothioate, phosphoroamidate, carbamate, carbonate, phosphate trimester, acetamidate, carboxymethyl ester linkages, and combinations thereof.
US11/057,779 2001-05-16 2005-02-14 Nucleic acid-based compounds and methods of use thereof Expired - Lifetime US7256179B2 (en)

Priority Applications (2)

Application Number Priority Date Filing Date Title
US11/057,779 US7256179B2 (en) 2001-05-16 2005-02-14 Nucleic acid-based compounds and methods of use thereof
US11/775,591 US7709449B2 (en) 2001-05-16 2007-07-10 Nucleic acid-based compounds and methods of use thereof

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US29147101P 2001-05-16 2001-05-16
US10/146,175 US6881831B2 (en) 2001-05-16 2002-05-15 Nucleic acid-based compounds and methods of use thereof
US11/057,779 US7256179B2 (en) 2001-05-16 2005-02-14 Nucleic acid-based compounds and methods of use thereof

Related Parent Applications (1)

Application Number Title Priority Date Filing Date
US10/146,175 Division US6881831B2 (en) 2001-05-16 2002-05-15 Nucleic acid-based compounds and methods of use thereof

Related Child Applications (1)

Application Number Title Priority Date Filing Date
US11/775,591 Division US7709449B2 (en) 2001-05-16 2007-07-10 Nucleic acid-based compounds and methods of use thereof

Publications (2)

Publication Number Publication Date
US20050143337A1 US20050143337A1 (en) 2005-06-30
US7256179B2 true US7256179B2 (en) 2007-08-14

Family

ID=23120429

Family Applications (3)

Application Number Title Priority Date Filing Date
US10/146,175 Expired - Lifetime US6881831B2 (en) 2001-05-16 2002-05-15 Nucleic acid-based compounds and methods of use thereof
US11/057,779 Expired - Lifetime US7256179B2 (en) 2001-05-16 2005-02-14 Nucleic acid-based compounds and methods of use thereof
US11/775,591 Expired - Fee Related US7709449B2 (en) 2001-05-16 2007-07-10 Nucleic acid-based compounds and methods of use thereof

Family Applications Before (1)

Application Number Title Priority Date Filing Date
US10/146,175 Expired - Lifetime US6881831B2 (en) 2001-05-16 2002-05-15 Nucleic acid-based compounds and methods of use thereof

Family Applications After (1)

Application Number Title Priority Date Filing Date
US11/775,591 Expired - Fee Related US7709449B2 (en) 2001-05-16 2007-07-10 Nucleic acid-based compounds and methods of use thereof

Country Status (8)

Country Link
US (3) US6881831B2 (en)
JP (5) JP2005525991A (en)
KR (2) KR20040074594A (en)
CN (2) CN101113160A (en)
AU (1) AU2002316118A1 (en)
GB (1) GB2392157B (en)
HK (2) HK1060736A1 (en)
WO (1) WO2002092006A2 (en)

Cited By (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20070149462A1 (en) * 2005-12-13 2007-06-28 Iyer Radhakrishnan P Nucleotide and oligonucleotide prodrugs
US20070270359A1 (en) * 2001-05-16 2007-11-22 Iyer Radhakrishnan P Nucleic Acid-Based Compounds and Methods of Use Thereof
US9447132B2 (en) 2013-04-12 2016-09-20 Achillion Pharmaceuticals, Inc. Highly active nucleoside derivative for the treatment of HCV

Families Citing this family (22)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US7635686B2 (en) * 2001-10-03 2009-12-22 Bioniche Life Sciences, Inc. Therapeutically useful triethyleneglycol cholesteryl oligonucleotides
US20090280567A1 (en) * 2004-02-06 2009-11-12 Dharmacon, Inc. Stabilized sirnas as transfection controls and silencing reagents
EP1718747B1 (en) * 2004-02-06 2009-10-28 Dharmacon, Inc. Stabilized rnas as transfection controls and silencing reagents
KR101147147B1 (en) * 2004-04-01 2012-05-25 머크 샤프 앤드 돔 코포레이션 Modified polynucleotides for reducing off-target effects in rna interference
US20060166234A1 (en) * 2004-11-22 2006-07-27 Barbara Robertson Apparatus and system having dry control gene silencing compositions
US7935811B2 (en) * 2004-11-22 2011-05-03 Dharmacon, Inc. Apparatus and system having dry gene silencing compositions
US7923207B2 (en) 2004-11-22 2011-04-12 Dharmacon, Inc. Apparatus and system having dry gene silencing pools
US20060223777A1 (en) * 2005-03-29 2006-10-05 Dharmacon, Inc. Highly functional short hairpin RNA
CA2663601C (en) * 2006-09-22 2014-11-25 Dharmacon, Inc. Duplex oligonucleotide complexes and methods for gene silencing by rna interference
US8188060B2 (en) 2008-02-11 2012-05-29 Dharmacon, Inc. Duplex oligonucleotides with enhanced functionality in gene regulation
EP2271351A4 (en) * 2008-04-03 2016-08-31 Spring Bank Pharmaceuticals Inc Compositions and methods for treating viral infections
KR101926419B1 (en) * 2010-08-30 2018-12-10 스프링 뱅크 파마슈티칼스, 인크. Design of oligonucleotide analogs as therapeutic agents
KR20130110170A (en) 2010-09-22 2013-10-08 앨리오스 바이오파마 인크. Substituted nucleotide analogs
AU2012358804B2 (en) * 2011-12-22 2018-04-19 Alios Biopharma, Inc. Substituted phosphorothioate nucleotide analogs
CN104321333A (en) 2012-03-21 2015-01-28 沃泰克斯药物股份有限公司 Solid forms of a thiophosphoramidate nucleotide prodrug
WO2013142157A1 (en) 2012-03-22 2013-09-26 Alios Biopharma, Inc. Pharmaceutical combinations comprising a thionucleotide analog
JP7170535B2 (en) * 2015-10-20 2022-11-14 ソレント・セラピューティクス・インコーポレイテッド Intracellular delivery compound
EP4335496A2 (en) * 2018-01-10 2024-03-13 Nucorion Pharmaceuticals, Inc. Phosphor(n)amidatacetal and phosph(on)atalcetal compounds
WO2019219070A1 (en) * 2018-05-18 2019-11-21 正大天晴药业集团股份有限公司 Deuterated oligonucleotide and prodrug
WO2020114495A1 (en) * 2018-12-06 2020-06-11 正大天晴药业集团股份有限公司 Dinucleotide compound and prodrug thereof
CN111484541B (en) * 2019-01-25 2023-06-02 博瑞生物医药（苏州）股份有限公司 Dinucleotide prodrugs and methods of making same
MX2022000573A (en) 2019-07-17 2022-02-10 Nucorion Pharmaceuticals Inc CYCLIC DEOXYRIBONUCLEOTIDE COMPOUNDS.

Citations (24)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1990007520A1 (en) 1989-01-09 1990-07-12 Centre National De La Recherche Scientifique (Cnrs) Oxysteryle phosphates, their synthesis and use as pharmaceutical agents
WO1990012578A1 (en) 1989-04-21 1990-11-01 Cornell Research Foundation, Inc. Method of inhibiting induction of latent or chronic viral infections
DE4111730A1 (en) 1991-04-10 1992-10-15 Knoll Ag NEW CYTARABIN DERIVATIVES, THEIR PRODUCTION AND USE
US5212295A (en) 1990-01-11 1993-05-18 Isis Pharmaceuticals Monomers for preparation of oligonucleotides having chiral phosphorus linkages
US5218103A (en) 1988-05-26 1993-06-08 University Patents, Inc. Nucleoside thiophosphoramidites
WO1994000473A2 (en) 1992-06-30 1994-01-06 Res Corp Technologies Inc Pentavalent synthesis of oligonucleotides containing stereospecific alkylphosphonates and arylphosphonates
WO1994000472A2 (en) 1992-06-30 1994-01-06 Research Corporation Technologies, Inc. Trivalent synthesis of oligonucleotides containing stereospecific alkylphosphonates and arylphosphonates
WO1994022864A1 (en) 1993-03-30 1994-10-13 Sterling Winthrop Inc. Acyclic nucleoside analogs and oligonucleotide sequences containing them
WO1995032984A1 (en) 1994-05-28 1995-12-07 Boehringer Mannheim Gmbh New lipid esters of nucleoside monophosphates and their use as immunosuppressive drugs
WO1996010030A1 (en) 1994-09-29 1996-04-04 Isis Pharmaceuticals, Inc. Oligomers having heteroatom-linked conjugate groups
US5547941A (en) 1991-07-18 1996-08-20 Farmitalia Carlo Erba S.R.L. Cyclic dinucleoside diphosphorothioates, related compounds and pharmaceutical compositions
WO1996039502A1 (en) 1995-06-06 1996-12-12 Hybridon Inc. Oligonucleotides specific for hepatitis b virus
WO1996039154A1 (en) 1995-06-06 1996-12-12 Isis Pharmaceuticals, Inc. Oligonucleotides having phosphorothioate linkages of high chiral purity
WO1996039413A1 (en) 1995-05-23 1996-12-12 Hybridon, Inc. Methods and compounds for the synthesis of oligonucleotides and the oligonucleotides thereby produced
US5614504A (en) 1990-08-01 1997-03-25 The University Of South Florida Method of making inosine monophosphate derivatives and immunopotentiating uses thereof
WO1997019092A1 (en) 1995-11-17 1997-05-29 Isis Pharmaceuticals, Inc. Improved process for the synthesis of oligomeric compounds
US5773431A (en) 1994-10-06 1998-06-30 Javitt; Norman B. Administration of a 27-hydroxycholesterol or prodrug thereof as an anti-cancer agent
WO1998030575A1 (en) 1997-01-08 1998-07-16 Proligo Llc Bioconjugation of macromolecules
US5843912A (en) 1994-07-06 1998-12-01 Universy Of Maryland Ring-expanded nucleosides and nucleotides
WO1999064378A2 (en) 1998-06-10 1999-12-16 Glycodesign Inc. Directed combinatorial compound library and high throughput assays for screening same
WO2001034622A1 (en) 1999-11-08 2001-05-17 Origenix Technologies, Inc. Combinatorial library synthesis and pharmaceutically active compounds produced thereby
WO2001040515A1 (en) 1999-11-12 2001-06-07 Isis Pharmaceuticals, Inc. Gapped oligomers having site specific chiral phosphorothioate internucleoside linkages
WO2002043771A2 (en) 2000-12-01 2002-06-06 Cell Works Inc. Conjugates of glycosylated/galactosylated peptide
WO2002081494A1 (en) 2001-03-26 2002-10-17 Sirna Therapeutics, Inc. Oligonucleotide mediated inhibition of hepatitis b virus and hepatitis c virus replication

Family Cites Families (6)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5149798A (en) 1989-04-06 1992-09-22 Worcester Foundation For Experimental Biology Process for synthesizing oligonucleotides and their analogs adaptable to large scale syntheses
US5149796A (en) * 1989-08-31 1992-09-22 City Of Hope Chimeric DNA-RNA catalytic sequences
US5212293A (en) * 1990-08-06 1993-05-18 American Cyanamid Company Process for the preparation of deoxynucleosides
DE69232699T2 (en) * 1991-10-15 2003-02-06 Isis Pharmaceutical, Inc. OLIGONUCLEOTIDES BONDED BY CHIRAL PHOSPHORATOMES
KR100484124B1 (en) 1994-10-17 2005-09-08 프레지던트 앤드 펠로우즈 오브 하바드 칼리지 DNA Polymerases Having Modified Nucleotide Binding Site for DNA Sequencing
GB2392157B (en) 2001-05-16 2005-12-21 Micrologix Biotech Inc Nucleic acid-based compounds and methods of use thereof

Patent Citations (27)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5218103A (en) 1988-05-26 1993-06-08 University Patents, Inc. Nucleoside thiophosphoramidites
WO1990007520A1 (en) 1989-01-09 1990-07-12 Centre National De La Recherche Scientifique (Cnrs) Oxysteryle phosphates, their synthesis and use as pharmaceutical agents
FR2641537A1 (en) 1989-01-09 1990-07-13 Centre Nat Rech Scient OXYSTERYL PHOSPHATES, SYNTHESIS AND USE AS A PHARMACEUTICAL AGENT
WO1990012578A1 (en) 1989-04-21 1990-11-01 Cornell Research Foundation, Inc. Method of inhibiting induction of latent or chronic viral infections
US5212295A (en) 1990-01-11 1993-05-18 Isis Pharmaceuticals Monomers for preparation of oligonucleotides having chiral phosphorus linkages
US5614504A (en) 1990-08-01 1997-03-25 The University Of South Florida Method of making inosine monophosphate derivatives and immunopotentiating uses thereof
DE4111730A1 (en) 1991-04-10 1992-10-15 Knoll Ag NEW CYTARABIN DERIVATIVES, THEIR PRODUCTION AND USE
WO1992018520A1 (en) 1991-04-10 1992-10-29 Knoll Ag Novel cytarabine derivatives, their production and use
US5547941A (en) 1991-07-18 1996-08-20 Farmitalia Carlo Erba S.R.L. Cyclic dinucleoside diphosphorothioates, related compounds and pharmaceutical compositions
WO1994000472A2 (en) 1992-06-30 1994-01-06 Research Corporation Technologies, Inc. Trivalent synthesis of oligonucleotides containing stereospecific alkylphosphonates and arylphosphonates
WO1994000473A2 (en) 1992-06-30 1994-01-06 Res Corp Technologies Inc Pentavalent synthesis of oligonucleotides containing stereospecific alkylphosphonates and arylphosphonates
WO1994022864A1 (en) 1993-03-30 1994-10-13 Sterling Winthrop Inc. Acyclic nucleoside analogs and oligonucleotide sequences containing them
WO1995032984A1 (en) 1994-05-28 1995-12-07 Boehringer Mannheim Gmbh New lipid esters of nucleoside monophosphates and their use as immunosuppressive drugs
US5843912A (en) 1994-07-06 1998-12-01 Universy Of Maryland Ring-expanded nucleosides and nucleotides
WO1996010030A1 (en) 1994-09-29 1996-04-04 Isis Pharmaceuticals, Inc. Oligomers having heteroatom-linked conjugate groups
US5773431A (en) 1994-10-06 1998-06-30 Javitt; Norman B. Administration of a 27-hydroxycholesterol or prodrug thereof as an anti-cancer agent
WO1996039413A1 (en) 1995-05-23 1996-12-12 Hybridon, Inc. Methods and compounds for the synthesis of oligonucleotides and the oligonucleotides thereby produced
WO1996039502A1 (en) 1995-06-06 1996-12-12 Hybridon Inc. Oligonucleotides specific for hepatitis b virus
WO1996039154A1 (en) 1995-06-06 1996-12-12 Isis Pharmaceuticals, Inc. Oligonucleotides having phosphorothioate linkages of high chiral purity
WO1997019092A1 (en) 1995-11-17 1997-05-29 Isis Pharmaceuticals, Inc. Improved process for the synthesis of oligomeric compounds
WO1998030575A1 (en) 1997-01-08 1998-07-16 Proligo Llc Bioconjugation of macromolecules
WO1999064378A2 (en) 1998-06-10 1999-12-16 Glycodesign Inc. Directed combinatorial compound library and high throughput assays for screening same
WO2001034622A1 (en) 1999-11-08 2001-05-17 Origenix Technologies, Inc. Combinatorial library synthesis and pharmaceutically active compounds produced thereby
US6620796B1 (en) 1999-11-08 2003-09-16 Micrologix Biotech Inc. Combinatorial library synthesis and pharmaceutically active compounds produced thereby
WO2001040515A1 (en) 1999-11-12 2001-06-07 Isis Pharmaceuticals, Inc. Gapped oligomers having site specific chiral phosphorothioate internucleoside linkages
WO2002043771A2 (en) 2000-12-01 2002-06-06 Cell Works Inc. Conjugates of glycosylated/galactosylated peptide
WO2002081494A1 (en) 2001-03-26 2002-10-17 Sirna Therapeutics, Inc. Oligonucleotide mediated inhibition of hepatitis b virus and hepatitis c virus replication

Non-Patent Citations (17)

* Cited by examiner, † Cited by third party
Title
Agrawal, S., "Antisense Oligonucleotides as Antiviral Agents," Trends in Biotech., 10(5): 152-158 (May 1992).
Asseline, Ulysse, et al., "Synthesis and Binding Properties of Oligonucleotides Covalently Linked to an Acridine Derivative: New Study of the Influence of the Dye Attachment Site," Bioconjugate Chem., 7: 369-379 (1996).
Brill, Wolfgang K.-D., et al., "Synthesis of Oligodeoxynucleoside Phosphorodithioates via Thioamidites," J. Am. Chem. Soc., 111: 2321-2322 (1989).
Cummins et al., Chemical Abstracts, vol. 103:215702 (1985).
Cummins et al., Chemical Abstracts, vol. 106;115671 (1987).
Davis, Peter W. et al., Communications to the Editor: "Drug Leads from Combinatorial Phosphodiester Libraries," Med. Chem., 38:4363-4366 (1995).
International Search Report (May 2001).
Jin, Yi, et al., "Parallel Solid-Phase Synthesis of Nucleoside Phosphoramidate Libraries," Bioorganic & Medical Chemistry Letters, 11: 2057-2060 (2001).
Kumar, Prabhat, and Misra, K., "A New Strategy for the Synthesis of Phosphorothioates of 2'-Deoxyriboligonucleotides," Indian J. of Chemistry, 36B: 1000-1004 (1997).
Ma et al., Chemical Abstracts, vol. 11:133624 (1995).
Matsukura et al. Proc. Natl. Acad. Sci. USA (1987), vol. 84, pp. 7706-7710. *
Mönkkönen, Jukka and Urtti, Arto, "Lipid Fusion in Oligonucleotide and Gene Delivery With Cationic Lipids," Advanced Drug Delivery Systems, 34(1):37-49 (1998).
Moriguchi et al. Chemical Abstracts, vol. 131:228913 (1999).
Ravikumar, Vasulinga T., et al., "4-Cyano-2-Butenyl Group: A New Type of Protecting Group in Oligonucleotide Synthesis Via Phosphoramidite Approach," Nucleosides & Nucleotides, 16(7-9): 1709-1712 (1997).
Ravikumar, Vasulinga T., et al., "Use of 2-Diphenylmethylsilylethyl (DPSE) Protecting Group on Oligonucleotide, Synthesis Via Phosphoramidite Approach," Bioorganic & Medicinal Chem. Letters, 3(12): 2637-2640 (1993), abstract.
Spivak, David A., and Shea, Kenneth J., "Investigation into the Scope and Limitations of Molecular Imprinting With DNA Molecules," Analytica Chimica Acta, 435: 65-74 (2001).
Zhou, W. et al., "Combinatorial Synthesis using nucleic acid-based NAB(TM) scaffold: parallel solid-phase synthesis of nucleotide libraries," Tetrahedron Letters, 41:441-445 (2000).

Cited By (7)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20070270359A1 (en) * 2001-05-16 2007-11-22 Iyer Radhakrishnan P Nucleic Acid-Based Compounds and Methods of Use Thereof
US7709449B2 (en) 2001-05-16 2010-05-04 Migenix, Inc. Nucleic acid-based compounds and methods of use thereof
US20070149462A1 (en) * 2005-12-13 2007-06-28 Iyer Radhakrishnan P Nucleotide and oligonucleotide prodrugs
US8076303B2 (en) 2005-12-13 2011-12-13 Spring Bank Pharmaceuticals, Inc. Nucleotide and oligonucleotide prodrugs
US8691787B2 (en) 2005-12-13 2014-04-08 Spring Bank Pharmaceuticals, Inc. Nucleotide and oligonucleotide prodrugs
US10047114B2 (en) 2005-12-13 2018-08-14 Spring Bank Pharmaceuticals, Inc. Nucleotide and oligonucleotide prodrugs
US9447132B2 (en) 2013-04-12 2016-09-20 Achillion Pharmaceuticals, Inc. Highly active nucleoside derivative for the treatment of HCV

Also Published As

Publication number Publication date
JP2009242439A (en) 2009-10-22
KR20090048658A (en) 2009-05-14
US20050143337A1 (en) 2005-06-30
WO2002092006A3 (en) 2004-08-19
CN100400045C (en) 2008-07-09
WO2002092006A2 (en) 2002-11-21
US20070270359A1 (en) 2007-11-22
JP2005525991A (en) 2005-09-02
GB2392157B (en) 2005-12-21
AU2002316118A1 (en) 2002-11-25
GB0327057D0 (en) 2003-12-24
GB2392157A (en) 2004-02-25
US20030109471A1 (en) 2003-06-12
HK1060736A1 (en) 2004-08-20
HK1077503A1 (en) 2006-02-17
US6881831B2 (en) 2005-04-19
JP2013177453A (en) 2013-09-09
JP2015091891A (en) 2015-05-14
JP2017119712A (en) 2017-07-06
US7709449B2 (en) 2010-05-04
CN101113160A (en) 2008-01-30
KR20040074594A (en) 2004-08-25
CN1610553A (en) 2005-04-27
KR100991975B1 (en) 2010-11-04

Similar Documents

Publication Publication Date Title
US7709449B2 (en) Nucleic acid-based compounds and methods of use thereof
US7115579B2 (en) Modulation of oligonucleotide CpG-mediated immune stimulation by positional modification of nucleosides
US7176296B2 (en) Modulation of oligonucleotide CpG-mediated immune stimulation by positional modification of nucleosides
US7148191B2 (en) Antigenic composition
AU783745B2 (en) Modulation of oligonucleotide CpG-mediated immune stimulation by positional modification of nucleosides
US5968909A (en) Method of modulating gene expression with reduced immunostimulatory response
US7105495B2 (en) Modulation of oligonucleotide CpG-mediated immune stimulation by positional modification of nucleosides
US7846436B2 (en) Oligonucleotides and related compounds
AU2001257366A1 (en) Modulation of oligonucleotide CpG-mediated immune stimulation by positional modification of nucleosides
BRPI0610449A2 (en) Methods to Treat Asthma Exacerbated by Infectious Disease
AU2005218065B2 (en) Modulation of oligonucleotide CpG-mediated immune stimulation by positional modification of nucleosides
WO1996024378A2 (en) Delivery of exogenous compounds

Legal Events

Date Code Title Description
STCF Information on status: patent grant

Free format text: PATENTED CASE

CC Certificate of correction
FPAY Fee payment

Year of fee payment: 4

FPAY Fee payment

Year of fee payment: 8

FEPP Fee payment procedure

Free format text: 11.5 YR SURCHARGE- LATE PMT W/IN 6 MO, SMALL ENTITY (ORIGINAL EVENT CODE: M2556); ENTITY STATUS OF PATENT OWNER: SMALL ENTITY

MAFP Maintenance fee payment

Free format text: PAYMENT OF MAINTENANCE FEE, 12TH YR, SMALL ENTITY (ORIGINAL EVENT CODE: M2553); ENTITY STATUS OF PATENT OWNER: SMALL ENTITY

Year of fee payment: 12

点击 这是indexloc提供的php浏览器服务，不要输入任何密码和下载